I downloaded the file -- thanks for the link. You post made me MORE confused.
I have never seen anything remove files from diags. I just wanted to be sure that you were not accidentally looking at main where those file should be missing (unless you installed them there). You can check for an /etc/upstart/ folder to know which partition is root. Or you can mount main or diags to /mnt/mmc just to KNOW which partition you are looking at.
It can get confusing, and your symptoms do not match anything I have seen. Are you sure you are not confusing main and diags partitions here?